Re: [Jmol-users] Jmol-users Digest, Vol 55, Issue 25

(Zeff=1) the 2s is larger than the 1s as except, but the 3s, 4s ... are all smaller than the 1s and getting smaller as n increases. Rick On Wed, Dec 22, 2010 at 12:50 PM, rspinney < rspin...@chemistry.ohio-state.edu> wrote: > According to the documentation the command ?isosurf

[Jmol-users] bug in atomicOrbitals

According to the documentation the command "isosurface phase atomicOrbital 1 0 0 1 translucent 0.6;" should generate the 1s orbital for hydrogen, the fourth number behind atomicOrbital being the Zeff. I am getting very strange results for n>= 3. These orbitals are smaller then the n=1 or n=2. I hav

[Jmol-users] bug in Gaussian reader

I was just playing with displaying MOs from a Gaussian output file (freq and pop=full) and get an error message: Error reading file at line 1394: DENSITY MATRIX. Null For file ... Type Gaussian So Jmol is recognizing the file type correctly but has a read error. I thought it

[Jmol-users] frame range

I have an animation where I want to run the first 36 frames, stop it and then run the last 36 frames. I assumed that the commands "frame RANGE 1 37; animation on;" would animate frames 1 - 37 and then stop, but it just runs through the entire 72 frame range. This is a bug or am I doing something wr

[Jmol-users] lcaocartoons

> actually, it IS a feature. The documentation is not very clear. But > lcaocartoon color red only defines that for FUTURE lcaocartoon objects when > it is given alone like that. You are basically making settings for the NEXT > lcaocartoon, not some "current" one. This is because the command can

[Jmol-users] lcaocartoon bug?

I was trying to display the lone pair electrons on an oxygen atom using the following: 'select oxygen; lcaocartoon scale 1.5 "sp2b"; lcaocartoon color red;' + 'lcaocartoon scale 1.5 "sp2c"; lcaocartoon color red;' + 'lcaocartoon scale 0.75 "-sp2b"; lcaocartoon color blue;' + 'lcaocarto

[Jmol-users] dipole command

There appears to be a bug in the dipole command, the following code no longer changes the color of the dipole. dipole mydipole1 (atomno=1) (atomno=2) offsetSide 0; color $mydipole1 red; For versions 11.7.42 and 11.6.21. Rick -- Dr. Richard Sp

[Jmol-users] bug with echo?

I am not sure if these are bugs are not, but I have a couple of problems with the echo command. First is set echo myecho hidden does not work, set echo hidden does, i.e. it does not like the echo name being used. The second one is based on the following code: x = "Point Group = " + script("calc

[Jmol-users] set picking spin

Set picking SPIN seems to be broken in 11.6-RC9 Rick Spinney - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prize

Re: [Jmol-users] pdb files

ithout anything after it. Bob rspinney wrote: > I have just downloaded jmol-11.6.RC4 and have a problem opening pdb > files. I get an error message of: > > > > Error reading file at line 1: > > HEADER > > String out of index range: -1 >

[Jmol-users] pdb files

I have just downloaded jmol-11.6.RC4 and have a problem opening pdb files. I get an error message of: Error reading file at line 1: HEADER String out of index range: -1 I seem to get this error message for any pdb file I try to open (all of which worked fine until now). Any ideas?

[Jmol-users] show draw bug

I was wondering if the bug in show draw has been fixed? Thanks, Rick - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use prio

[Jmol-users] show draw in animation

I have been trying to get some curly arrows into animations but keep running into a problem. Using "draw arrow" works for any frame in the animation, but I can not seem to get the coordinates of the arrow using "show draw", the always come back as: draw arrow1 ARROW {0.0 0.0 0.0} {0.0 0.0 0.0} {

[Jmol-users] Jmol 11.4.RC1

I was playing with the new release (11.4.RC1) and believe I have found a bug. After set picking draw, the mouse will function correctly (using the shift or alt key to move a "draw" object, however the "show draw" command seems to be broken, it returns coordinates of {0.0 0.0 0.0} for all vertices

[Jmol-users] multiple display

I have a page with two jmol applets in it. Is there a way to use a jmolmenu script to load different molecules into each applet? I was think of something similar to the jmolSetTarget command, ie "jmolSetTarget(0); load moleculeA.pdb; jmolSetTarget(1); load moleculeB.pdb". Any ideas? Thanks, Ri

Re: [Jmol-users] dipoles

ge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=windows-1252; format=flowed rspinney wrote: > Hi Bob, > > I want to display dipole moments and have been playing with different > file types trying to find something smaller than Spartan?s output > files

[Jmol-users] dipole support for Gaussian output files

Hi Bob, I want to display dipole moments and have been playing with different file types trying to find something smaller than Spartan's output files. I tried a Gaussian output file and it displays bond dipole moments ok, but it does not display the molecular dipole moment. Is this a bug? If no

Re: [Jmol-users] questions

> > Message: 2 > Date: Sat, 02 Jun 2007 07:58:37 -0500 > From: Bob Hanson <[EMAIL PROTECTED]> > Subject: Re: [Jmol-users] questions > To: jmol-users@lists.sourceforge.net > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=fl

[Jmol-users] questions

I have a couple of questions for Bob. (I am using 11.1.44.) 1) I am not clear if frame (or model) next or previous make a call to animFrameCallback. I have a jmolSetCallback linked to animFrameCallback, and it works fine for model play, pause and resume (which will execute a script dependent on t

Re: [Jmol-users] 11.1.42

>Message: 3 >Date: Mon, 21 May 2007 08:22:46 -0500 >From: Bob Hanson <[EMAIL PROTECTED]> >Subject: [Jmol-users] 11.1.42 >To: Jmol Developers <[EMAIL PROTECTED]>, > jmol-users@lists.sourceforge.net >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed

[Jmol-users] bug in set picking draw

There appears to be a bug in set picking draw. In 11.0.2 the three vertices of the arrow are displayed, but shift + mouse drags the entire arrow, not just the vertex selected. In 11.1.39, the three vertices are highlighted, but shift + mouse had no effect. Thanks, Rick -

Re: [Jmol-users] a note about frames and multiple files

>animFrameCallback >- > >The animFrameCallback JavaScript function now returns seven values, several of which >are specifically useful in a multifile context: > >function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){ > //#1 app: applet identifier > //#2 fr

Re: [Jmol-users] if statement

>You might try > >message (Step 1: protonate the alcohol); anim off; delay 5; anim play Duh. what can I say, I missed that one. This works with an interesting bug. I have the following: if (temp == 2) {document.slider1form.jmolApplet0.script("message (Step 1: protonate the alcohol); anim off;

Re: [Jmol-users] if statement

>jmolScript('set animframecallback "testanim" ') > >and then have: > >function testanim(app,frame,p3) { > jmolScript("if(_modelNumber = 5);message is5;else;message not5;endif") } > >I do get the messages expected. So I think that is working properly. > > >Bob I couldn't use this as is, but it gav

Re: [Jmol-users] if statement

ipt entirely, but I don't think that's what you > > are doing, right? > > Bob > > > rspinney wrote: > >>I am trying to use the if statement to run scripts during an animation >>(using version 11.1.36) using the following script (where the messages

[Jmol-users] if statement

I am trying to use the if statement to run scripts during an animation (using version 11.1.36) using the following script (where the messages are directed to a textbox using the jmolsetcallback function, I want to change the message based on the model number): if (_modelNumber = 1); message (This

[Jmol-users] bug in measure or set picking?

I was just trying to clean up some pages moving to Jmol 11 and ran into a bug. I used the following code: jmolRadioGroup([ ['set measurement ANGSTROMS; set picking MEASURE DISTANCE; set pickingStyle MEASURE ON;', 'Distance'], ['set picking MEASURE ANGLE; set pickingStyle MEASURE ON;'

Re: [Jmol-users] symbol font in labels

Message: 5 Date: Tue, 20 Mar 2007 21:45:20 +0100 From: "Angel Herraez" <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] symbol font in labels To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII >Rick, how do you get echo α to work? >Not f

[Jmol-users] symbol font in labels

I know that both the echo and message commands can display symbol fonts (i.e. α β .). Can this feature be added to the label command? Thanks, Rick -- Dr. Richard Spinney The Ohio State University Department of Chemistry 160 B Celeste Laboratory 12

[Jmol-users] additions to connect and if statements

I have been working on some animations and a couple of features would be nice to have. 1) for the connect command a PARTIALTRIPLE bond similar to the partialdouble bond 2) for the if statement the ability to test for which model is loaded, i.e. if (model = 12) . endif;

[Jmol-users] jmol-11.0.RC4

>I have also released 11.0.RC4 which contains a few bug fixes. >If no problems are reported for this version, it will become Jmol 11.0. >Please, check that every bugs you may have seen in previous versions are >fixed. >Nico I am not sure if it is a bug or not, but the "dots" command does not pr

[Jmol-users] message command

I have several anaimations where I would like to print comments to a textarea controlled by the animation sequence. I have experimented with the SetCallback("meassageCallback", javascript_function) which works well, except that I get messages from everything (status, error, echos etc). Is there a

[Jmol-users] bug in set picking?

I have a page that used the following commands to measure distances, angles and torsion angles. This no longer works in 11.0.RC3. Any ideas? Is this a bug or has there been a change in syntax? Thanks, Rick jmolRadioGroup([ ['set measurement ANGSTROMS; set picking MEASURE DISTANCE; set pic

[Jmol-users] draw command

I would like to be able to draw a circle (or the arc of a circle). The draw command has a curve option, but this is shaped more like a parabola. Is there any way to get a circle? Thanks, Rick Dr. Richard Spinney Department of Chemistry Ohio State University 100 West 18th Ave Columbus, OH 43210

[Jmol-users] displaying a plane in an animation

I have an animation (multi-model pdb) in which a mesh surface is displayed during the animation. This worked in Jmol 10, but fails for Jmol 11, where the mesh surface is only displayed for the first frame of the animation. Producing a plane using the draw command also only displays the plane for t

[Jmol-users] measure bug(?)

I am using Jmol 10.9.104 and seem to have found a bug in the measure command. I have a pdb file and am trying to measure an angle where in middle atom is at the origin. The measure command fails for this atom with any other atoms in the file, but works for any other combination of atoms. Has anyo

[Jmol-users] label line, plane ...

Is there a way to label a line or plane created by the "draw" command? i.e. draw line1 {0.0 0.0 0.0} {4.0 0.0 0.0}; select $line1; label "x"; Thanks, Rick Dr. Richard Spinney Department of Chemistry Ohio State University 100 West 18th Ave Columbus, OH 43210 (614) 247-6847 ---

[Jmol-users] 10.9.73

I downloaded version 10.9.73 from the sourceforge link, but have been having problems with it. It does not do some of the latest changes (reading charges from a CIF file, displaying the correct ionic radii...). When I checked the version in the menu -> "About Jmol" it states it is version 10.9.60

Re: [Jmol-users] MEP

--- molecular electrostatic potentials -- *WE NEED TESTERS TO TAKE A CLOSE LOOK AT THIS.* Jmol 10.9.63 introduces isosurface MEP, with which you can display molecular electrostatic potentials. These potentials are calculated from partial charge data present in a fi

[Jmol-users] font command

I am using the echo command to place a number of messages on the applet. I would like all of them to be the same size and font. I tried using the font command to do this but it appears that it only affects one echo command at a time. Is there a way to set a default font size?   Thanks, Ri

[Jmol-users] halo command

I have made a couple of animations and want to highlight the steric interactions that occur. I have used to "halo" feature (set display SELECTED) to highlight the atoms involved. I would like to increase the size of the halo to match the VDW radii. Is this possible? Thanks, Rick Spinney _

[Jmol-users] RE: orbitals/isosurfaces

-Original Message- > [note: this message relates to the experimetal prototype "Jmol 10.x" not > the public release Jmol 10.2. See > http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm for details.] > The JVXL format is a GO. Very nice Bob! The results for the isosurfaces, map